Aleksandar Mehandzhiyski Virtual Simulation Lab seminar series www.virtualsiml...
Пікірлер: 52
@MsSADAFRANI6 жыл бұрын
Thank you for such a nice presentation. I was trying MD which was seemingly difficult for me. After seeing this presentation I got a lot of understanding. thank you so much
@nelsonbarrios17188 жыл бұрын
Thanks a lot for this excellent presentation 👍👍 It helped me to understand more about GROMACS
@aleksandarmehandzhiyski29648 жыл бұрын
Great, I am glad it was helpful. :)
@mzheleva7 жыл бұрын
Супер! Лекцията беше много полезна за изпълнението на моята първа симулация с GROMACS!
@aleksandarmehandzhiyski29647 жыл бұрын
Радвам се че видеото е било полезно за вас.
@sekekeretsu41726 жыл бұрын
YOU MADE IT LOOK SO EASY. PLEASE UPLOAD MORE OF YOUR WORKS .
@placidoism5 жыл бұрын
Hi Aleksandar, thanks a lot for your tutorial but a I have a big doubt. How have you created the file topol.top? You don't write any output comand with -o topol.top and suddendly you use it when solvate molecules. I am having a lot of problems with topology, a little help will be welcome. Thanks :D
@luiscarlosperez74263 жыл бұрын
same problem. Have you done yet ?
@explorewithashokgunturu2 жыл бұрын
I got the same problem while performing the simulation. After that, I saw couple of sample .top files and wrote one my own. I believe, the topol.top file has to be written by the person who performs the experiment.
@explorewithashokgunturu2 жыл бұрын
You can see the contents of topol.top file that has been used by him at 31:34. Just create a file with the name topol.top and write the displayed content on the file.
@ZohanSyahFatomi5 жыл бұрын
Nice tutorial, however if there is a subtitle in english that will be more much appreciated. :D
@gabco115 жыл бұрын
Great tutorial, thanks a lot !
@juliopdaniel7 жыл бұрын
Greetings from Brazil! I would like to see something about comparative modelling (i´m a begginer in computational biology). Thanks a lot for this presetantion!
@matchem91783 жыл бұрын
Thanks!
@EwelinaRutkowska7 жыл бұрын
Thank you for uploading this seminar. It is very helpful. Is there any repository from where the files of this trial can be downloaded?
@VirtualSimulationLab7 жыл бұрын
You can find all the materials on our webpage www.virtualsimlab.com
Can I simulate hydrogen plus oxygen gives water products to reactants with only telling number of Hydrogen atoms and oxygen atoms where the equations satisfy scrodinger equation so the reactants will give this product for checking every chemical equations without memorizing the equations please tell me if IAM wrong simply can I check the chemical equations even the sulphuric acid preparation reactions or uranium reactions or just combine two atoms and can I tell their products
@klusblody7 жыл бұрын
Gromacs for the win
@alejouchihasama2 жыл бұрын
good video, however I am doing it to the letter and an error appears when adding the ions, it says that there is an error in the recognition of the atoms ... for help. Thank you
@tannguyen12927 жыл бұрын
thanks you so much. Could we use one topol.top file for all molecule? or we must create a new topol.top for every molecule. Thanks
@farzanehahmadi11714 жыл бұрын
why I can’t produce mdp format in gromax? in all my reserch, see downlod links of ions. mdp for lyzozim. but i want produce that is or find mdp format for every protein. please, help me. thank you so much.
@rajendrakc59694 жыл бұрын
I don't know about producing, but you can definitely edit those MDP files as per your need
@sajadyaghoubizadeh84164 жыл бұрын
Hi guys, is it possible to simulate the bioabsorption process by GROMACS or any other MDS apps? it's necessary. Thx
@truongtonchu6 жыл бұрын
Can you show how to simulation CO2 with amine or ILs? Thank you
@wenchongzhou26015 жыл бұрын
Why we have to adjust the order of atom coordinates at 23.05? Can anyone please tell me, many thanks!
@19neetish4 жыл бұрын
because charges were wrong. The script only predicts the type of atom and in the case prediction was wrong.
@rangkhuray23055 жыл бұрын
i running umbrella sampling. but i don't have file complex.gro. how i can get the file? thank you for your answer,.
@zoizwitsa96275 жыл бұрын
you can search in this site for configuration atb.uq.edu.au/index.py and then use editconf in gromacs to produce your complex.gro file
@AliceFan-je1dm5 ай бұрын
senior intellectuals
@nijatshukurov9022 Жыл бұрын
I cant find topolgen file.
@PharmaAI-LearningCenter4 жыл бұрын
Please guide me on how to run MD on gromacs with GPU. Running MD on GPU showing error
@susmitaroy38994 жыл бұрын
You may use command (-nb gpu) for example gmx mdrun - v - deffnm em - nb gpu I hope it helps...
@AxlSPPDgame4 жыл бұрын
So, the link page doesnt work anymore??
@aleksandarmehandzhiyski29644 жыл бұрын
It does not work at the moment. The page is supposed to be updated.
@RakeshBhowmick5 жыл бұрын
Can I run a simulation of 50k atom in my desktop pc having i5 processor for 20ns
@markjack6865 жыл бұрын
Yes, you can. but I think you will cost a few days for running if you have not use GPU acceleration.
@asmauhamza2884 жыл бұрын
Please what is GPU acceleration
@asmauhamza2884 жыл бұрын
Please what is GPU acceleration
@sangeetakhargharia87524 жыл бұрын
Can someone suggest me some papers on which these types of works are done..
is there any supporting information in this paper i couldn't found it?
@aleksandarmehandzhiyski29644 жыл бұрын
No, there is no SI.
@umakantapradhan13275 жыл бұрын
hiiiii thnx for the tutorial. I am beginner to GROMACS. I was unable to understand how u got the all the ions.mdp , md.mdp , mdout.mdp , minim.mdp , newbox.mdp , npt.mdp , nvt.mdp , posre.itp , topol.top. Please help!!!!!!!
@aleksandarmehandzhiyski29645 жыл бұрын
Hi, all of these files are simple text files, which I have created some time ago, and just reuse/modify whenever I need them. You can find the files used in the presentation in the Virtual Sim Lab webpage.
@umakantapradhan13275 жыл бұрын
@@aleksandarmehandzhiyski2964.... can u teach me how can i generate or create all the ions.mdp , md.mdp , mdout.mdp , minim.mdp , newbox.mdp , npt.mdp , nvt.mdp , posre.itp , topol.top for my molecule.
@umakantapradhan13275 жыл бұрын
@@aleksandarmehandzhiyski2964 sir I am still waiting for your reply. Can I have your email id for better communication about GROMACS.
@computational_biophysics4 жыл бұрын
Greetings sir, where can i download this presentation?